Detailed prediction of protein sub-nuclear localization

BMC Bioinformatics

Table 2 Comparison between LocNuclei and NSort

Sub-nuclear compartment	Number of proteins	AUC NSort	AUC LocNuclei-NSort
Perinucleolar	24	0.80 ± 0.05	0.73 ± 0.03
Cajal body	49	0.60 ± 0.03	0.62 ± 0.02
Nuclear pore complex	51	0.79 ± 0.05	0.88 ± 0.02
Nuclear lamina	77	0.70 ± 0.01	0.82 ± 0.01
PML bodies	91	0.77 ± 0.03	0.75 ± 0.01
Chromatin	323	0.71 ± 0.01	0.78 ± 0.01
Nuclear speckle	403	0.71 ± 0.01	0.77 ± 0.01
Nucleolus	598	0.60 ± 0.01	0.72 ± 0.01
Sum/Mean	1285	0.71 ± 0.03	0.76 ± 0.02

For this comparison, LocNuclei was re-trained using the development data of NSort, comprising 1285 sequence-unique proteins annotated in eight sub-nuclear localization classes. On proteins from all eight classes, LocNuclei performed equally well as or better than NSort except for proteins located in the perinucleolar. The overall cross-validated AUC of LocNuclei was 0.76 compared to 0.71 for NSort. The values for NSort were taken from its publication [12]

ISSN: 1471-2105